In apples, four cytoplasmic groups, 'Golden Delicious'-, 'Delicious'-, 'McIntosh'- and 'Dolgo Crab' cytotypes, are differentiated by variation in the mitochondrial cox1 and atp9 loci. The present study builds upon previous reports that (1) 'Golden Delicious' and 'Delicious' cytotype accessions each contain an intact cox1 (named as G-cox1 and D-cox1, respectively) and a pseudocopy (G-Psi cox1 and D-Psi cox1) at different stoichiometries and (2) the relative copy number of an atp9 pseudocopy (Psi atp9-1) is distinct in each cytotype. Here, the D-cox1 and D-Psi cox1 sequences were found as predominant forms in 'McIntosh' type germplasm accessions but as substoichiometric forms in 'Dolgo Crab' type accessions. The G-cox1 and G-Psi cox1 sequences were predominant in the 'Dolgo Crab' group whereas these two sequences were substoichiometric in the 'McIntosh' group. 'We also detected the presence of predominant form of Psi atp9-1 in 'McIntosh' and 'Dolgo Crab' groups. Moreover, the four cytotypes could be distinguished from one another by their own chloroplast DNA haplotypes. Using these data and those from our earlier publications, we attempted to construct a network of cytotypes representing possible maternal lineages of apples. (C) 2013 Elsevier B.V. All rights reserved.